2023
Mistranslation of the genetic code by a new family of bacterial transfer RNAs
Schuntermann D, Fischer J, Bile J, Gaier S, Shelley B, Awawdeh A, Jahn M, Hoffman K, Westhof E, Söll D, Clarke C, Vargas-Rodriguez O. Mistranslation of the genetic code by a new family of bacterial transfer RNAs. Journal Of Biological Chemistry 2023, 299: 104852. PMID: 37224963, PMCID: PMC10404621, DOI: 10.1016/j.jbc.2023.104852.Peer-Reviewed Original ResearchMeSH KeywordsAmino AcidsCodonEscherichia coliGenetic CodeHumansMutationProlineProtein BiosynthesisProteinsProteomeRNA, TransferStreptomycesThreonineConceptsTransfer RNAsAmino acidsBacterial transfer RNAsUnfavorable environmental conditionsProlyl-tRNA synthetaseWrong amino acidPoor substrate specificitySubstrate discriminationGrowth defectTransfer RNAGenetic codePosttranslational modificationsProtein reporterTranslation factorsEnvironmental stressFunctional proteinsSubstrate specificityThreonine codonGenetic informationDistinct isoformsPro mutationAntibiotic carbenicillinEscherichia coliNovel familyEnvironmental conditionsSplit aminoacyl-tRNA synthetases for proximity-induced stop codon suppression
Jiang H, Ambrose N, Chung C, Wang Y, Söll D, Tharp J. Split aminoacyl-tRNA synthetases for proximity-induced stop codon suppression. Proceedings Of The National Academy Of Sciences Of The United States Of America 2023, 120: e2219758120. PMID: 36787361, PMCID: PMC9974479, DOI: 10.1073/pnas.2219758120.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acyl-tRNA SynthetasesCodon, TerminatorEscherichia coliHumansLigasesProtein BiosynthesisRNA, TransferConceptsAminoacyl-tRNA synthetasesCodon suppressionStop codon suppressionGene expressionOrthogonal aminoacyl-tRNA synthetasesRelevant protein-protein interactionsSynthetic biology toolsSmall molecule rapamycinControl gene expressionProtein-protein interactionsLevel of transcriptionAbscisic acidDimerization domainMammalian cellsBiology toolsGene translationTranslational levelMolecular switchStop codonHuman cellsMolecular inputsUseful biotechnologySynthetasesExpressionTherapeutic applications
2022
Uncovering translation roadblocks during the development of a synthetic tRNA
Prabhakar A, Krahn N, Zhang J, Vargas-Rodriguez O, Krupkin M, Fu Z, Acosta-Reyes FJ, Ge X, Choi J, Crnković A, Ehrenberg M, Puglisi EV, Söll D, Puglisi J. Uncovering translation roadblocks during the development of a synthetic tRNA. Nucleic Acids Research 2022, 50: 10201-10211. PMID: 35882385, PMCID: PMC9561287, DOI: 10.1093/nar/gkac576.Peer-Reviewed Original ResearchMeSH KeywordsAmino AcidsAmino Acyl-tRNA SynthetasesNucleotidesProtein BiosynthesisRibosomesRNA, TransferSelenocysteineConceptsOrthogonal translation systemGenetic code expansionCode expansionTertiary interactionsNon-canonical amino acidsAminoacyl-tRNA substratesDomains of lifeAminoacyl-tRNA synthetaseTranslation systemSingle nucleotide mutationsSingle-molecule fluorescenceDistinct tRNAsNon-canonical structuresSelenocysteine insertionRibosomal translationTRNARibosomesSynthetic tRNANucleotide mutationsAmino acidsSame organismP siteOrganismsTranslocationTranslationMeasuring the tolerance of the genetic code to altered codon size
DeBenedictis EA, Söll D, Esvelt KM. Measuring the tolerance of the genetic code to altered codon size. ELife 2022, 11: e76941. PMID: 35293861, PMCID: PMC9094753, DOI: 10.7554/elife.76941.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acyl-tRNA SynthetasesAnticodonCodonEscherichia coliGenetic CodeProtein BiosynthesisRNA, TransferConceptsFour-base codonsGenetic codeTRNA mutationsAminoacyl-tRNA synthetasesQuadruplet codonsSingle amino acidCodon translationTriplet codonsTRNA synthetasesSynthetic biologistsCodonTRNAAmino acidsChemical alphabetsMutationsMass spectrometrySynthetasesAnticodonToleranceSynthetic systemsBiologistsTranslationEscherichiaNascent
2018
Transfer RNA function and evolution
O’Donoghue P, Ling J, Söll D. Transfer RNA function and evolution. RNA Biology 2018, 15: 423-426. PMID: 30099966, PMCID: PMC6103721, DOI: 10.1080/15476286.2018.1478942.Peer-Reviewed Original Research
2008
Quality control despite mistranslation caused by an ambiguous genetic code
Ruan B, Palioura S, Sabina J, Marvin-Guy L, Kochhar S, LaRossa RA, Söll D. Quality control despite mistranslation caused by an ambiguous genetic code. Proceedings Of The National Academy Of Sciences Of The United States Of America 2008, 105: 16502-16507. PMID: 18946032, PMCID: PMC2575449, DOI: 10.1073/pnas.0809179105.Peer-Reviewed Original ResearchMeSH KeywordsEscherichia coliGenetic CodeHeat-Shock ResponseMass SpectrometryMutation, MissenseProtein BiosynthesisRNA, Transfer, Amino AcylConceptsGenetic codeAa-tRNAWild-type proteinAminoacyl-tRNA synthetasesInactive mutant proteinsHeat shock responseE. coliMutant proteinsReporter proteinMissense suppressionFunctional proteinsCognate tRNASelective pressureAminoacyl-tRNAActive enzymeShock responseProtein synthesisNative conformationEnergetic costAmino acidsMissense mutationsProteinBiochemical evidenceCorrect pairingProtein quality
2004
Cys-tRNACys formation and cysteine biosynthesis in methanogenic archaea: two faces of the same problem?
Ambrogelly A, Kamtekar S, Sauerwald A, Ruan B, Tumbula-Hansen D, Kennedy D, Ahel I, Söll D. Cys-tRNACys formation and cysteine biosynthesis in methanogenic archaea: two faces of the same problem? Cellular And Molecular Life Sciences 2004, 61: 2437-2445. PMID: 15526152, DOI: 10.1007/s00018-004-4194-9.Peer-Reviewed Original ResearchConceptsMethanogenic archaeaCysteine biosynthesisCellular translation machineryAminoacyl-tRNA synthesisCanonical cysteinyl-tRNA synthetaseAminoacyl-tRNA synthetasesCysteinyl-tRNA synthetaseRecognizable genesTranslation machineryGenome sequenceArchaeaBiosynthesisEssential componentSynthetasesTRNARibosomesGenesMachineryOrganismsSynthetasePossible linkSequenceFormation
2001
A dual‐specific Glu‐tRNAGln and Asp‐tRNAAsn amidotransferase is involved in decoding glutamine and asparagine codons in Acidithiobacillus ferrooxidans
Salazar J, Zúñiga R, Raczniak G, Becker H, Söll D, Orellana O. A dual‐specific Glu‐tRNAGln and Asp‐tRNAAsn amidotransferase is involved in decoding glutamine and asparagine codons in Acidithiobacillus ferrooxidans. FEBS Letters 2001, 500: 129-131. PMID: 11445070, DOI: 10.1016/s0014-5793(01)02600-x.Peer-Reviewed Original ResearchConceptsOperon-like structureGlutaminyl-tRNA synthetaseGlutamyl-tRNA synthetaseA. ferrooxidansAsparaginyl-tRNA synthetaseTransamidation pathwayGat genesGlu-tRNAGlnBioleaching of mineralsAsn-tRNAAcidithiobacillus ferrooxidansGln-tRNAAsparagine codonsSynthetase enzymeBacillus subtilisAcidophilic bacteriumEscherichia coliBiochemical analysisAmidotransferaseSynthetaseGenesProtein synthesis: Twenty three amino acids and counting
Ibba M, Stathopoulos C, Söll D. Protein synthesis: Twenty three amino acids and counting. Current Biology 2001, 11: r563-r565. PMID: 11509255, DOI: 10.1016/s0960-9822(01)00344-x.Peer-Reviewed Original ResearchGenomics and the evolution of aminoacyl-tRNA synthesis.
Ruan B, Ahel I, Ambrogelly A, Becker H, Bunjun S, Feng L, Tumbula-Hansen D, Ibba M, Korencic D, Kobayashi H, Jacquin-Becker C, Mejlhede N, Min B, Raczniak G, Rinehart J, Stathopoulos C, Li T, Söll D. Genomics and the evolution of aminoacyl-tRNA synthesis. Acta Biochimica Polonica 2001, 48: 313-21. PMID: 11732603, DOI: 10.18388/abp.2001_3917.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acyl-tRNA SynthetasesEvolution, MolecularGenomicsPhylogenyProtein BiosynthesisRNA, MessengerRNA, Transfer, Amino AcylConceptsAminoacyl-tRNA synthesisAminoacyl-tRNA synthetasesTransfer RNAsAmino acidsMessenger RNAGenetic informationContemporary aminoacyl-tRNA synthetasesDirect protein synthesisNon-canonical routesEvolutionary diversityEvolutionary divergenceCys-tRNANascent polypeptidesRibosome movesAsn-tRNAGln-tRNAWhole genomeAppropriate amino acidsTRNA anticodonSubstrate specificityLys-tRNATrinucleotide codonsNext codonUnexpected levelProtein synthesisThe renaissance of aminoacyl‐tRNA synthesis
Ibba M, Söll D. The renaissance of aminoacyl‐tRNA synthesis. EMBO Reports 2001, 2: 382-387. PMID: 11375928, PMCID: PMC1083889, DOI: 10.1093/embo-reports/kve095.Peer-Reviewed Original ResearchMeSH KeywordsAmino AcidsAmino Acyl-tRNA SynthetasesAnimalsArchaeaBacteriaEvolution, MolecularProtein BiosynthesisRNA, Transfer, Amino AcylConceptsAminoacyl-tRNA synthesisProtein synthesisRole of tRNAEvolutionary diversityStructural biologyMolecular biologistsUnexpected arrayMolecular biologyNew enzymeDecades of studyAmino acidsEssential processTRNABiologyComplete pictureGenomicsAdaptorBiologistsDiversityEnzymePathwayHigh degreeSynthesisNumerous milestones
2000
The Adaptor hypothesis revisited
Ibba M, Becker H, Stathopoulos C, Tumbula D, Söll D, Ibba M, Becker H, Stathopoulos C, Tumbula D, Söll D. The Adaptor hypothesis revisited. Trends In Biochemical Sciences 2000, 25: 311-316. PMID: 10871880, DOI: 10.1016/s0968-0004(00)01600-5.Peer-Reviewed Original Research
1997
Glu-tRNAGln amidotransferase: A novel heterotrimeric enzyme required for correct decoding of glutamine codons during translation
Curnow A, Hong K, Yuan R, Kim S, Martins O, Winkler W, Henkin T, Söll D. Glu-tRNAGln amidotransferase: A novel heterotrimeric enzyme required for correct decoding of glutamine codons during translation. Proceedings Of The National Academy Of Sciences Of The United States Of America 1997, 94: 11819-11826. PMID: 9342321, PMCID: PMC23611, DOI: 10.1073/pnas.94.22.11819.Peer-Reviewed Original ResearchConceptsTranscriptional unitsGln-tRNAGlnGram-positive eubacteriaHeterotrimeric enzymeGlu-tRNAGlnTranslational apparatusHeterotrimeric proteinGlutamine codonB. subtilisAmidotransferaseSynthetase activityOnly pathwayEnzymeGlutamylEssential componentArchaeaTransamidationEubacteriaOperonCyanobacteriaGATCOrganellesCodonGenesGATAA nuclear genetic lesion affecting Saccharomyces cerevisiae mitochondrial translation is complemented by a homologous Bacillus gene
Kim S, Stange-Thomann N, Martins O, Hong K, Söll D, Fox T. A nuclear genetic lesion affecting Saccharomyces cerevisiae mitochondrial translation is complemented by a homologous Bacillus gene. Journal Of Bacteriology 1997, 179: 5625-5627. PMID: 9287027, PMCID: PMC179443, DOI: 10.1128/jb.179.17.5625-5627.1997.Peer-Reviewed Original ResearchMeSH KeywordsBacillus subtilisDNA, FungalDNA, MitochondrialFungal ProteinsGenes, BacterialMitochondrial ProteinsMolecular Sequence DataProtein BiosynthesisRecombinant Fusion ProteinsSaccharomyces cerevisiaeSaccharomyces cerevisiae ProteinsSequence Analysis, DNASequence Homology, Amino AcidTransaminasesTranscription Factors
1995
Aminoacylation of transfer RNAs with 2-thiouridine derivatives in the wobble position of the anticodon
Rogers K, Crescenzo A, Söll D. Aminoacylation of transfer RNAs with 2-thiouridine derivatives in the wobble position of the anticodon. Biochimie 1995, 77: 66-74. PMID: 7541255, DOI: 10.1016/0300-9084(96)88106-5.Peer-Reviewed Original ResearchConceptsEvolution of specificityPost-transcriptional modificationsAnticodon of tRNAAminoacyl-tRNA synthetasesTranslational regulationTransfer RNAWobble positionWobble baseLysine tRNATRNAEscherichia coliAnticodonAminoacylationFirst positionSynthetasesRNAColiRegulationGlutamineModificationDiscoveryGlutamate
1994
A point mutation in Euglena gracilis chloroplast tRNA(Glu) uncouples protein and chlorophyll biosynthesis.
Stange-Thomann N, Thomann H, Lloyd A, Lyman H, Söll D. A point mutation in Euglena gracilis chloroplast tRNA(Glu) uncouples protein and chlorophyll biosynthesis. Proceedings Of The National Academy Of Sciences Of The United States Of America 1994, 91: 7947-7951. PMID: 8058739, PMCID: PMC44521, DOI: 10.1073/pnas.91.17.7947.Peer-Reviewed Original ResearchMeSH KeywordsAldehyde OxidoreductasesAnimalsBase SequenceBlotting, NorthernChlorophyllChloroplastsCloning, MolecularDNADNA PrimersEuglena gracilisIntramolecular TransferasesIsomerasesMolecular Sequence DataNucleic Acid ConformationPoint MutationPolymerase Chain ReactionProtein BiosynthesisRNA, Transfer, GluConceptsEuglena gracilis chloroplastsChlorophyll biosynthesisGlu-tRNA reductaseChlorophyll-deficient mutantsPoint mutationsChloroplast protein synthesisSequence-specific mannerDual-function moleculeC5 pathwayNADPH-dependent reductionSpecific cofactorsGluTRFirst enzymeGene productsUniversal precursorImportant identity elementAminomutase activitySequence analysisE. gracilisSecond enzymeTetrapyrrole pigmentsT-loopProtein synthesisBiosynthesisChloroplasts
1992
Synthetase competition and tRNA context determine the in vivo identity of tRNA discriminator mutants
Sherman J, Rogers K, Rogers M, Söll D. Synthetase competition and tRNA context determine the in vivo identity of tRNA discriminator mutants. Journal Of Molecular Biology 1992, 228: 1055-1062. PMID: 1474577, DOI: 10.1016/0022-2836(92)90314-a.Peer-Reviewed Original ResearchConceptsAmber suppressorTyrosine tRNAN-terminal protein sequencingGlutamyl-tRNA synthetaseE. coli dihydrofolate reductaseAminoacyl-tRNA synthetasesEffects of mutationsEfficiency of aminoacylationColi dihydrofolate reductaseSite of aminoacylationTyrosine specificityTRNAs exhibitGlutamine tRNAMutagenic analysisProtein sequencingGlutamate tRNAImportant identity elementVivo identityTRNANucleotide substitutionsTRNA identityDiscriminator baseDihydrofolate reductaseMultiple mutationsSynthetases
1990
Expression of the Synechocystis sp. strain PCC 6803 tRNA(Glu) gene provides tRNA for protein and chlorophyll biosynthesis
O'Neill G, Söll D. Expression of the Synechocystis sp. strain PCC 6803 tRNA(Glu) gene provides tRNA for protein and chlorophyll biosynthesis. Journal Of Bacteriology 1990, 172: 6363-6371. PMID: 2121711, PMCID: PMC526821, DOI: 10.1128/jb.172.11.6363-6371.1990.Peer-Reviewed Original ResearchConceptsSynechocystis 6803Synechocystis spFirst anticodon baseStrain PCC 6803Cyanobacterium Synechocystis spTotal tRNA populationAmount of chlorophyllNorthern blot analysisChlorophyll biosynthesisALA biosynthesisPrecursor tRNAsPCC 6803TRNA speciesProtein biosynthesisTRNA populationCellular RNAAminoacylation assaysChlorophyll levelsBiosynthesisAddition of inhibitorsBlot analysisTranslation systemDelta-aminolevulinic acidTRNAChlorophyll
1989
Characterization of cis-acting mutations which increase expression of a glnS-lacZ fusion in Escherichia coli
Plumbridge J, Söll D. Characterization of cis-acting mutations which increase expression of a glnS-lacZ fusion in Escherichia coli. Molecular Genetics And Genomics 1989, 216: 113-119. PMID: 2471922, DOI: 10.1007/bf00332238.Peer-Reviewed Original Research
1988
Discrimination between glutaminyl-tRNA synthetase and seryl-tRNA synthetase involves nucleotides in the acceptor helix of tRNA.
Rogers M, Söll D. Discrimination between glutaminyl-tRNA synthetase and seryl-tRNA synthetase involves nucleotides in the acceptor helix of tRNA. Proceedings Of The National Academy Of Sciences Of The United States Of America 1988, 85: 6627-6631. PMID: 3045821, PMCID: PMC282030, DOI: 10.1073/pnas.85.18.6627.Peer-Reviewed Original Research